I bought mine in 2010 (its a 2008 model though) and I am still using stock seat. Longest we rode was a 1100 miles round trip with one night stop over. The stock seat did not fare too bad. It was much more comfortable to my wife, but was causing problem for me towards the end of the journey. I run the stock windshield, which is shorter than the 2010 up windshield, during the summer months. Full down, no buffeting, but you get a good blast of wind (most welcomed) on your torso. Full up, it is quieter, but get some helmet buffeting. For the other months, I have a cee baily euro that serves me good - very quite and no buffeting. Just a bit too warm in the cockpit during summer.
Any bike you get, you have to do some adjustments based on your riding style, your comfort, etc - especially one that you will be touring on. For me, the windshield and a pair of handlebar raisers did the trick. Seat will be nice, but so far, the stock seat is not that much of a problem - not enough to plunk $500 for a custom seat. For some, the foot pegs had to be lowered.
Regarding the buffeting problem your wife experienced, was there was cross wind or something that day? I will have to ask my wife if she experiences buffeting all the time - she never complained to me once, but who knows !
The only thing I like about the FJR is the cruise control - but C14 any day any time.